rs10115304
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001174147.2(LMX1B):c.1107C>A(p.Ser369Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S369S) has been classified as Benign.
Frequency
Consequence
NM_001174147.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMX1B | NM_001174147.2 | c.1107C>A | p.Ser369Arg | missense_variant | 8/8 | ENST00000373474.9 | |
LMX1B | NM_001174146.2 | c.1119C>A | p.Ser373Arg | missense_variant | 8/8 | ||
LMX1B | NM_002316.4 | c.1086C>A | p.Ser362Arg | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMX1B | ENST00000373474.9 | c.1107C>A | p.Ser369Arg | missense_variant | 8/8 | 1 | NM_001174147.2 | P4 | |
LMX1B | ENST00000355497.10 | c.1119C>A | p.Ser373Arg | missense_variant | 8/8 | 1 | |||
LMX1B | ENST00000526117.6 | c.1086C>A | p.Ser362Arg | missense_variant | 8/8 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251328Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135864
GnomAD4 exome AF: 0.0000794 AC: 116AN: 1461780Hom.: 0 Cov.: 32 AF XY: 0.0000715 AC XY: 52AN XY: 727212
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at